Genome-wide discovery of small RNAs in Mycobacterium tuberculosis.

Only few small RNAs (sRNAs) have been characterized in Mycobacterium tuberculosis and their role in regulatory networks is still poorly understood. Here we report a genome-wide characterization of sRNAs in M. tuberculosis integrating experimental and computational analyses. Global RNA-seq analysis o...

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Autores principales:	Paolo Miotto, Francesca Forti, Alessandro Ambrosi, Danilo Pellin, Diogo F Veiga, Gabor Balazsi, Maria L Gennaro, Clelia Di Serio, Daniela Ghisotti, Daniela M Cirillo
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/807f5aa603544be88cf3e2ea6fdab75a
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spelling	oai:doaj.org-article:807f5aa603544be88cf3e2ea6fdab75a2021-11-18T08:04:30ZGenome-wide discovery of small RNAs in Mycobacterium tuberculosis.1932-620310.1371/journal.pone.0051950https://doaj.org/article/807f5aa603544be88cf3e2ea6fdab75a2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23284830/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Only few small RNAs (sRNAs) have been characterized in Mycobacterium tuberculosis and their role in regulatory networks is still poorly understood. Here we report a genome-wide characterization of sRNAs in M. tuberculosis integrating experimental and computational analyses. Global RNA-seq analysis of exponentially growing cultures of M. tuberculosis H37Rv had previously identified 1373 sRNA species. In the present report we show that 258 (19%) of these were also identified by microarray expression. This set included 22 intergenic sRNAs, 84 sRNAs mapping within 5'/3' UTRs, and 152 antisense sRNAs. Analysis of promoter and terminator consensus sequences identified sigma A promoter consensus sequences for 121 sRNAs (47%), terminator consensus motifs for 22 sRNAs (8.5%), and both motifs for 35 sRNAs (14%). Additionally, 20/23 candidates were visualized by Northern blot analysis and 5' end mapping by primer extension confirmed the RNA-seq data. We also used a computational approach utilizing functional enrichment to identify the pathways targeted by sRNA regulation. We found that antisense sRNAs preferentially regulated transcription of membrane-bound proteins. Genes putatively regulated by novel cis-encoded sRNAs were enriched for two-component systems and for functional pathways involved in hydrogen transport on the membrane.Paolo MiottoFrancesca FortiAlessandro AmbrosiDanilo PellinDiogo F VeigaGabor BalazsiMaria L GennaroClelia Di SerioDaniela GhisottiDaniela M CirilloPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 12, p e51950 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Paolo Miotto Francesca Forti Alessandro Ambrosi Danilo Pellin Diogo F Veiga Gabor Balazsi Maria L Gennaro Clelia Di Serio Daniela Ghisotti Daniela M Cirillo Genome-wide discovery of small RNAs in Mycobacterium tuberculosis.
description	Only few small RNAs (sRNAs) have been characterized in Mycobacterium tuberculosis and their role in regulatory networks is still poorly understood. Here we report a genome-wide characterization of sRNAs in M. tuberculosis integrating experimental and computational analyses. Global RNA-seq analysis of exponentially growing cultures of M. tuberculosis H37Rv had previously identified 1373 sRNA species. In the present report we show that 258 (19%) of these were also identified by microarray expression. This set included 22 intergenic sRNAs, 84 sRNAs mapping within 5'/3' UTRs, and 152 antisense sRNAs. Analysis of promoter and terminator consensus sequences identified sigma A promoter consensus sequences for 121 sRNAs (47%), terminator consensus motifs for 22 sRNAs (8.5%), and both motifs for 35 sRNAs (14%). Additionally, 20/23 candidates were visualized by Northern blot analysis and 5' end mapping by primer extension confirmed the RNA-seq data. We also used a computational approach utilizing functional enrichment to identify the pathways targeted by sRNA regulation. We found that antisense sRNAs preferentially regulated transcription of membrane-bound proteins. Genes putatively regulated by novel cis-encoded sRNAs were enriched for two-component systems and for functional pathways involved in hydrogen transport on the membrane.
format	article
author	Paolo Miotto Francesca Forti Alessandro Ambrosi Danilo Pellin Diogo F Veiga Gabor Balazsi Maria L Gennaro Clelia Di Serio Daniela Ghisotti Daniela M Cirillo
author_facet	Paolo Miotto Francesca Forti Alessandro Ambrosi Danilo Pellin Diogo F Veiga Gabor Balazsi Maria L Gennaro Clelia Di Serio Daniela Ghisotti Daniela M Cirillo
author_sort	Paolo Miotto
title	Genome-wide discovery of small RNAs in Mycobacterium tuberculosis.
title_short	Genome-wide discovery of small RNAs in Mycobacterium tuberculosis.
title_full	Genome-wide discovery of small RNAs in Mycobacterium tuberculosis.
title_fullStr	Genome-wide discovery of small RNAs in Mycobacterium tuberculosis.
title_full_unstemmed	Genome-wide discovery of small RNAs in Mycobacterium tuberculosis.
title_sort	genome-wide discovery of small rnas in mycobacterium tuberculosis.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/807f5aa603544be88cf3e2ea6fdab75a
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Genome-wide discovery of small RNAs in Mycobacterium tuberculosis.

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